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- PDB-4g4o: MutM containing M77A mutation bound to oxoG-containing DNA -

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Basic information

Entry
Database: PDB / ID: 4g4o
TitleMutM containing M77A mutation bound to oxoG-containing DNA
Components
  • DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*(8OG)P*AP*GP*(TX2)P*CP*TP*AP*CP*C)-3')
  • DNA (5'-D(P*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)-3')
  • Formamidopyrimidine-DNA glycosylaseDNA-formamidopyrimidine glycosylase
KeywordsHydrolase/DNA / DNA glycosylase / DNA repair / lesion recognition / base extrusion / disulfide crosslinking / Hydrolase-DNA complex
Function / homology
Function and homology information


DNA-formamidopyrimidine glycosylase / oxidized purine nucleobase lesion DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc ion binding
Similarity search - Function
Formamidopyrimidine-DNA glycosylase / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins ...Formamidopyrimidine-DNA glycosylase / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13-like, H2TH / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSung, R.J. / Zhang, M. / Qi, Y. / Verdine, G.L.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural and Biochemical Analysis of DNA Helix Invasion by the Bacterial 8-Oxoguanine DNA Glycosylase MutM.
Authors: Sung, R.J. / Zhang, M. / Qi, Y. / Verdine, G.L.
History
DepositionJul 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Formamidopyrimidine-DNA glycosylase
B: DNA (5'-D(P*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)-3')
C: DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*(8OG)P*AP*GP*(TX2)P*CP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4614
Polymers40,3963
Non-polymers651
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-16 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.188, 93.541, 104.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Formamidopyrimidine-DNA glycosylase / DNA-formamidopyrimidine glycosylase / Fapy-DNA glycosylase / DNA-(apurinic or apyrimidinic site) lyase MutM


Mass: 30522.229 Da / Num. of mol.: 1 / Fragment: MutM / Mutation: M77A, Q166C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: mutM / Production host: Escherichia coli (E. coli)
References: UniProt: P84131, DNA-formamidopyrimidine glycosylase
#2: DNA chain DNA (5'-D(P*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)-3')


Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*(8OG)P*AP*GP*(TX2)P*CP*TP*AP*CP*C)-3')


Mass: 4925.275 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8K, sodium cacodylate, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→32.685 Å / Num. obs: 31863
Reflection shellResolution: 1.95→2.01 Å / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→32.685 Å / SU ML: 0.16 / σ(F): 0.21 / Phase error: 18.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 1583 4.97 %
Rwork0.1752 --
obs0.1769 31863 96.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.355 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8768 Å2-0 Å2-0 Å2
2---0.0376 Å20 Å2
3----1.8393 Å2
Refinement stepCycle: LAST / Resolution: 1.95→32.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 539 1 219 2747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072692
X-RAY DIFFRACTIONf_angle_d1.1073753
X-RAY DIFFRACTIONf_dihedral_angle_d18.3871067
X-RAY DIFFRACTIONf_chiral_restr0.064413
X-RAY DIFFRACTIONf_plane_restr0.004398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.01290.24431160.19132485X-RAY DIFFRACTION88
2.0129-2.08490.21081210.17442622X-RAY DIFFRACTION92
2.0849-2.16830.19851300.16982694X-RAY DIFFRACTION94
2.1683-2.2670.19191340.16642712X-RAY DIFFRACTION96
2.267-2.38650.20881670.16932693X-RAY DIFFRACTION96
2.3865-2.53590.19861470.17322744X-RAY DIFFRACTION97
2.5359-2.73170.2261690.18782743X-RAY DIFFRACTION98
2.7317-3.00640.22151540.19272813X-RAY DIFFRACTION98
3.0064-3.4410.22361500.182836X-RAY DIFFRACTION99
3.441-4.33370.20121500.15642902X-RAY DIFFRACTION99
4.3337-32.68920.19831450.17263036X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.0943-0.0489-0.18221.12551.09161.01570.0013-0.02620.0343-0.0106-0.10510.058-0.062-0.0510.09040.08570.0091-0.01930.1226-0.04240.119913.8615-4.305417.1085
26.0568-2.0337-3.59535.68131.44152.146-0.7-0.6876-0.13660.83450.41720.91520.2172-0.04380.26430.4010.01860.05170.3953-0.00080.39743.8643-12.358327.805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B OR CHAIN C

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